Pramesh Singh

An interpretable alphabet for local protein structure search based on amino acid neighborhoods

The paper introduces a new structural alphabet for protein structure search that improves accuracy when combined with existing methods.

Rapid, high-resolution, non-destructive assessments of metabolic and morphological homogeneity uniquely identify high-grade cervical precancerous lesions

This paper uses two-photon microscopy to detect high-grade cervical precancerous lesions with high sensitivity and specificity by analyzing metabolic and morphological features.

Identification of Disease Modules Using Higher-Order Network Structure

The paper introduces a higher-order community detection method to identify disease modules in protein-protein interaction networks and GWAS data, revealing new disease-associated modules not found by conventional methods.

Accuracy of functional gene community detection in Saccharomyces cerevisiae by maximizing Generalized Modularity Density

The paper compares twelve methods for inferring gene co-expression networks and identifying functional communities in yeast, finding that CLR followed by Generalized Modularity Density clustering performs best.

Identifying robust functional modules using three-body correlations in Escherichia coli

The paper identifies robust functional gene modules in Escherichia coli using three-body correlations and community detection in gene co-expression networks.

Stop Bickering! Reconciling Signaling Pathway Databases with Network Topologies

This paper quantifies structural differences in signaling pathway databases by analyzing their topological properties and shows that pathways have database-specific characteristics.